How Bad Gut Bacteria Influence Cravings, Mood, and Eating Habits

Are Bad Gut Bacteria Controlling Your Cravings?

You’re doing your best—trying to eat clean, stay on track, and tune in to your body. But suddenly, out of nowhere, the craving hits. Chips, sugar, takeout… something salty, sweet, or starchy. And it’s not just a passing thought—it feels like an urge. Almost like something else is calling the shots.

That “something else” might be your gut microbiome—specifically, the overgrowth of harmful bacteria that can influence your food choices, your mood, and even your motivation. In this post, we’ll break down the fascinating science behind how gut microbes send signals to your brain, why cravings are often a microbial imbalance (not a willpower problem), and how restoring balance in the gut can lead to clearer thinking and more nourishing choices—naturally.

This post is part of our Gut Healing Series — a 12-part journey into the hidden roots of digestive imbalance and the natural path back to balance. From microbiome repair to herbal remedies, mindful fasting, and daily rhythms that support your gut-brain connection, each article offers practical steps rooted in science and tradition.

Explore the full series here

The Gut-Brain Connection 101

Your gut and brain are in constant communication, thanks to a powerful network called the gut-brain axis. At the center of this conversation is the vagus nerve, a long, wandering nerve that acts like a two-way radio—carrying messages back and forth between your digestive system and your brain. This isn’t just a metaphor. About 90% of the communication along the vagus nerve travels from the gut to the brain, not the other way around.

This means your gut is influencing your thoughts, feelings, and decisions more than you might realize. And the messengers behind many of those signals are your gut microbes—the trillions of bacteria, yeast, and other organisms living in your digestive tract. Some of them are helpful: they produce neurotransmitters like serotonin (which helps regulate mood), dopamine (linked to motivation and reward), and GABA (which promotes calm and focus). They also help produce short-chain fatty acids that reduce inflammation and keep your gut lining strong.

But when your gut is overrun with pathogenic or opportunistic bacteria, the conversation changes. These “bad” microbes thrive on processed sugars and refined carbs—and when they dominate, they can hijack your internal messaging system. They send signals that increase hunger, amplify cravings for the foods they prefer, and disrupt your body's natural satiety cues. At the same time, they can interfere with neurotransmitter balance, contributing to low mood, irritability, anxiety, or even a foggy, impulsive state that makes healthy choices feel harder than they should.

The result? You’re not just craving chips or sweets—you’re being influenced at a biochemical level by an imbalanced ecosystem. And until the balance is restored, willpower alone may never feel like enough.

What Are “Bad” Gut Bacteria?

Not all bacteria are bad—your gut is home to trillions of microbes, many of which help you digest food, produce vitamins, regulate immune function and even influence your mood. But when these unhelpful microbes gain the upper hand, it leads to dysbiosis an imbalance in your gut microbiome that often shows up as bloating, cravings, brain fog, anxiety and more.

These so-called “bad” bacteria aren’t inherently evil; they’re just opportunistic. They thrive when we eat a highly processed diet, live under chronic stress, or take repeated courses of antibiotics. Once they gain a foothold, they can disrupt digestion, increase inflammation, and even influence your behavior by hijacking communication between your gut and brain.

Researchers have identified certain microbial troublemakers that are especially good at surviving off of sugar and processed food. These include:

• Clostridium difficile – (very nasty) known for causing inflammation and gut dysbiosis
• Klebsiella – linked to cravings, bloating, and immune issues
• Desulfovibrio – produces inflammatory byproducts in the gut
• Enterobacter and Citrobacter – associated with poor metabolic health
• Overgrowth of certain E. coli strains – can further disrupt gut balance

You don’t need to memorize their names—but knowing they exist helps explain why you might feel out of control around certain foods. The more sugar and refined carbs you eat, the more fuel these microbes get, reinforcing the cycle of cravings, bloating, and mood swings.

And it’s not just bacteria. Opportunistic yeasts, like candida albicans, can also overgrow and contribute to the problem. These microbes are incredibly adaptive—they’re not just passively living in your digestive tract. They’re active participants, working to keep themselves alive and well-fed in any way they can.

One of the ways they do this is by releasing chemical messengers—signals that can influence your hunger hormones and mood. In other words, they can trigger cravings for the very foods they need to survive: sugar, simple carbs, processed snacks, and starchy comfort foods.

This is one of the most overlooked reasons why cravings feel so strong—and why it often feels like you’re working against yourself. You’re not necessarily craving what your body needs… you’re craving what your imbalanced gut microbiome is asking for.

And when these bacteria are in control, they don’t just influence what you eat. They can also affect how you feel, think, and respond. Over time, this microbial imbalance can impact serotonin and dopamine levels, which are closely tied to mood, focus, and even your ability to make clear decisions around food.

Until you begin to shift the internal ecosystem—reducing the fuel source for these organisms and bringing in foods and herbs that support balance—those messages can continue to shape your decisions, emotions, and eating patterns day after day.

How Cravings Are Manufactured

Cravings often feel like they come out of nowhere, but they’re actually the result of complex signaling systems—many of which start in the gut. When the microbiome is imbalanced, those signals become distorted, and the body starts asking for what will feed the imbalance, not nourish you.

One major player in this process is the vagus nerve—the main communication line between your gut and brain. Harmful gut bacteria and yeasts can send signals through this nerve that influence how hungry you feel, what you crave, and even your emotional state around food. At the same time, they can trigger the release of inflammatory cytokines, which are chemical messengers that promote low-grade inflammation and contribute to mood swings, brain fog, and an increased drive to seek out comfort foods.

The result is a powerful feedback loop that keeps you reaching for quick fuel. As dysbiosis worsens, it disrupts normal gut hormone production—especially hormones like ghrelin (which stimulates hunger) and leptin (which signals fullness). You might find yourself eating more but never really feeling satisfied, or constantly grazing just to keep your energy up.

On top of that, poor microbial balance contributes to unstable blood sugar, which makes cravings even more intense. Blood sugar crashes are often interpreted by the body as an emergency—prompting a spike in hunger hormones and driving the urge for fast-acting carbs.

And then there’s stress. Chronic stress doesn’t just affect your mindset—it directly impacts your gut health. Stress increases gut permeability (aka “leaky gut”), shifts microbial populations, and activates the same hormonal systems that make you crave sugar, caffeine, or comfort food. This creates a vicious cycle: the more stressed you are, the more your gut suffers... and the more your gut suffers, the harder it becomes to make nourishing choices.

But here’s the hopeful side of cravings: they don’t always mean something is wrong. When the gut is balanced and your systems are working well, cravings can actually be a helpful signal from your body. For example, a sudden craving for something hearty like red meat might reflect a need for iron, zinc, or B12—nutrients that can also be found in plant-based sources or supplements. A pull toward leafy greens may signal a need for magnesium or folate. The point is: when your microbiome is in balance, your body becomes better at guiding you toward what it truly needs—without the confusion, urgency, or emotional charge that dysbiosis often brings.

The Emotional Eating Loop

If you’ve ever found yourself reaching for sugar or comfort food when you're overwhelmed, tired, anxious, or sad—you’re not alone. And you’re not broken. Emotional eating isn’t just about willpower or bad habits—it’s often a biological loop fueled by an imbalanced gut and a dysregulated nervous system.

Here’s how it works:
An unhealthy microbiome can lead to mood instability—low energy, irritability, brain fog, or anxious thoughts. When those feelings surface, the brain naturally seeks relief. It turns to what it knows will create a quick dopamine spike or sense of comfort—usually sugar, refined carbs, or caffeine. That temporary reward may feel like it helps in the moment, but it also feeds the very microbes that contributed to the emotional imbalance in the first place.

As those microbes grow stronger, they send out more chemical signals that trigger cravings and amplify emotional volatility. Your body gets caught in a loop: mood swings → cravings → more sugar → deeper gut imbalance → repeat.

It’s a cycle that can feel hard to escape—especially when you're trying to make better choices, but your biology is pulling you in a different direction.

Breaking this loop requires more than just resisting the craving in the moment. Real change comes from working at the root—supporting the body in a way that helps you feel emotionally grounded and biologically balanced.

That means addressing two core systems at the same time:

1. The gut, by crowding out harmful microbes and bringing in the foods, herbs, and nutrients that support microbial balance.
2. The nervous system, through consistent practices like eating in a way that keeps energy stable, moving your body regularly, getting restorative sleep, and using simple calming activities to reduce stress-driven patterns.

When both systems are supported, something shifts. The urgent cravings start to quiet down. Emotional spikes feel less extreme. And healthy choices begin to feel more natural—less like a fight and more like a return to balance.

Rebalancing Your Gut = Reclaiming Control

This is how you break the cycle.

When you understand that cravings, mood swings, and low energy aren’t personal failings—but signals of gut imbalance—you can stop battling your body and start working with it. By supporting your gut and nervous system, you interrupt the feedback loop that keeps you stuck. The clearer your inner signals become, the easier it is to make nourishing choices without the constant push-pull of willpower.

Here’s where that reset begins:

1. Eat to support your gut, not your cravings.

Build meals around fiber-rich vegetables, clean proteins, and healthy fats. This helps stabilize blood sugar and mood while nourishing beneficial microbes—and depriving the ones that thrive on sugar and processed food. Over time, this shifts your internal ecosystem in a more balanced direction, without needing to be overly restrictive.

2. Use herbs and beneficial bacteria to guide the shift.

Bitters, antimicrobials, and gut-soothing herbs can help reduce overgrowth and inflammation. When appropriate, probiotic foods or supplements can reintroduce balance and diversity. These natural tools are most effective when used strategically and consistently.

3. Give your gut time to self-clean.

The migrating motor complex (MMC) is your gut’s internal housekeeping system—it activates between meals to sweep away debris and discourage bacterial buildup. Meal spacing or a gentle intermittent fasting window (like 18:6) allows this process to function optimally.

4. Calm the system that controls digestion.

Your nervous system plays a central role in digestion and gut repair. Chronic stress keeps you in a state of dysregulation—slowing digestion, weakening immunity, and fueling cravings. Even small shifts like breathwork, meditation, walking, restorative sleep, or screen-free time can send signals of safety to your body and support healing from the inside out.

Final Thoughts: Your Gut, Your Power

Your cravings aren't random. Your mood swings, your energy crashes, your compulsive snack habits—these are all part of a deeper conversation happening inside your body. When your gut is out of balance, it doesn’t just affect digestion—it influences your brain, your emotions and your decisions.

But the most important takeaway is this: you can shift it.

Healing your gut isn’t about willpower or perfection. It’s about building an internal environment that works for you instead of against you—one that makes it easier to feel calm, clear, and in control. When you support your microbiome, nourish your body with real food, and regulate your nervous system, you create the conditions for lasting change.

Change your gut, and your mind will follow.

Curious About What This Could Look Like for You?

If you’d like to go deeper, explore the step-by-step system inside the Laguna Gut Protocol. It’s a gentle, food- and herb-based reset that helps you rebalance your gut, reduce cravings, and reclaim your energy—without extremes or overwhelm.

With care for your gut and mind,
Cole
Laguna Beach Apothecary

Keep listening to your body—it’s wiser than you think.